Compose is very idiocyncratic, as you have discovered. What you merge are files. Compose , I think, will only let you have one file in that left window. If you open a file and then read , it is in there, open a second, and read, it replaces the first one. Open a second, click merge, and read and it will put both files together. The only way to do this group by group is if they are each a separate file. Once you have a merged file, you have several options re: what you save. If you click on object - then you save the whole K&K . If you click on a group under object, or CTRL click on a complex of them, then this will be what you save. I am going to step back a bit and say this though - I do not think that there is an advantage to be had in making a single multilayered object and there is a major disadvantage. The skin IS going to poke thru the clothing in some poses, and in a merged figure, there ain't much you can do about it. With conforming clothing, there is. This technique is pre the latest patches, when you could not save multi figures in a CR2. IF however, you are replacing the hip, thighs, and shins with a clothing mesh, this does have its advantages - no poke thru, smaller mesh.